A fully reproducible and state-of-the-art ancient DNA analysis pipeline
A tool to infer metagenomic sample composition
This repository contains practical data analyses exercises for the special course on Paleogenomics and Anthropology held at the National School of Anthropology of Mexico (ENAH), May 6 to 10, 2019. Topics include performing QC on aDNA NGS data, assigning mtDNA haplogroups and testing hypotheses w/PCA and ADMIXTURE analyses. No previous command-li...
🧹🦷 aKmerBroom: Ancient oral DNA decontamination using Bloom filters on k-mer sets
A free and easy-to-use pipeline to analyse data from ancient NCR-mtDNA sequences obtained by amplicon-based NGS methods
A Snakemake-based pipeline for processing and quality-controlling ancient and historical DNA data, including taxonomic assessment and comparative genomic analysis across time points, producing damage-rescaled, mapped reads ready for downstream analyses.
Electronic protocol files (Hamilton NGS STAR workstation) for indexing PCR setup and purification of indexed libraries using Solid Phase Reversible Immobilization (SPRI) technology (deAngelis et al. 1995).
Electronic protocol files (Hamilton NGS STAR workstation) for TWIST hybridization capture of DNA libraries.
Perl scripts for reconstructing the structure of double-stranded DNA fragments from single-stranded DNA libraries
Electronic protocol files (Hamilton NGS STAR workstation) for in-solution hybridization capture of ssDNA libraries.
Electronic protocol files (Bravo NGS workstation B) for the ssDNA2.0 library preparation method (Gansauge et al. 2020).
An automated snakemake pipeline designed to benchmark the classification performance and accuracy of previously published aDNA genetic kinship estimation methods.
Perform hard selective masking of ancient DNA deamination patterns, using the output misincorporation frequency estimates of MapDamage (https://ginolhac.github.io/mapDamage/)
Script and utilities applied to perform kinship analysis between ancient Mentesh-Tepe individuals, found in (Garino-Vignon, P., et al 2023)
Raw code to get polymorphisms from samples analysed by using the PowerSeq® CRM Nested System kit (Promega Corporation)
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